Package: segmentSeq

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch segmentSeq_1.4.0.tar.gz

StartedAt: 2011-10-20 17:18:59 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 17:32:18 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 798.5 seconds

RetCode: 0

Status:  OK

CheckDir: segmentSeq.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/segmentSeq.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'segmentSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'segmentSeq' version '1.4.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'segmentSeq' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under inst/doc ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'segmentSeq' ...
** R
** inst
** preparing package for lazy loading
Creating a generic for 'cbind' in package 'segmentSeq'
    (the supplied definition differs from and overrides the implicit generic
    in package 'base': Signatures differ:  (...), (deparse.level))
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (segmentSeq)

name	user	system	elapsed
alignmentData-class	4.598	0.317	4.926
classifySeg	96.727	3.222	100.471
filterSegments	51.283	2.150	53.836
findChunks	5.014	0.490	5.527
getCounts	4.983	0.432	5.690
getOverlaps	4.807	0.419	5.549
heuristicSeg	65.130	2.711	69.475
lociLikelihoods	65.092	2.716	70.025
mergeSD	105.473	4.185	113.135
plotGenome	4.104	0.401	4.551
processAD	51.803	1.903	54.431
processTags	4.259	0.465	5.134
segData-class	53.776	2.125	56.540
segmentSeq-package	52.767	2.078	55.286